Genomes and Genes
Summary: Changes in biological features that help an organism cope with its ENVIRONMENT. These changes include physiological (ADAPTATION, PHYSIOLOGICAL), phenotypic and genetic changes.
Publications247 found, 100 shown here
- Adaptive protein evolution in DrosophilaNick G C Smith
Centre for the Study of Evolution and School of Biological Sciences, University of Sussex, Brighton BN1 9QG, UK
Nature 415:1022-4. 2002..yakuba. We estimate that 45% of all amino-acid substitutions have been fixed by natural selection, and that on average one adaptive substitution occurs every 45 years in these species...
- The genetic theory of adaptation: a brief historyH Allen Orr
Department of Biology, University of Rochester, Rochester, New York 14627, USA
Nat Rev Genet 6:119-27. 2005..I also discuss the challenges that face contemporary theories of adaptation...
- Biological robustnessHiroaki Kitano
Sony Computer Science Laboratories, Inc, 3 14 13 Higashi Gotanda, Shinagawa, Tokyo 141 0022, Japan
Nat Rev Genet 5:826-37. 2004..Insights into inherent properties of robust systems will provide us with a better understanding of complex diseases and a guiding principle for therapy design...
- Perspective: Evolution and detection of genetic robustnessJ Arjan G M de Visser
Department of Genetics, Wageningen University, Arboretumlaan 4, 6703 BD Wageningen, The Netherlands
Evolution 57:1959-72. 2003....
- Evolution experiments with microorganisms: the dynamics and genetic bases of adaptationSantiago F Elena
Instituto de Biologia Molecular y Celular de Plantas, Consejo Superior de Investigaciones Cientificas, 46022 Valencia, Spain
Nat Rev Genet 4:457-69. 2003....
- Adaptive evolution drives divergence of a hybrid inviability gene between two species of DrosophilaDaven C Presgraves
Department of Biology, University of Rochester, Rochester, New York 14627, USA
Nature 423:715-9. 2003..These results show that a lethal hybrid incompatibility has evolved as a by-product of adaptive protein evolution...
- An equivalence principle for the incorporation of favorable mutations in asexual populationsMatthew Hegreness
Bauer Center for Genomics Research, Harvard University, Cambridge, MA 02138, USA
Science 311:1615-7. 2006..The effective parameters constitute a simple description and provide a natural standard for comparing adaptation between species and across environments...
- Co-mimics have a mutualistic relationship despite unequal defencesHannah M Rowland
School of Biological Sciences, University of Liverpool, Biosciences Building, Crown Street, Liverpool L69 7ZB, UK
Nature 448:64-7. 2007..By ignoring the effects of density, current theories may have overestimated the parasitic costs imposed by less defended mimics on highly defended models...
- Genome-wide patterns of nucleotide substitution reveal stringent functional constraints on the protein sequences of thermophilesRobert Friedman
Department of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208, USA
Genetics 167:1507-12. 2004....
- Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolutionM Anisimova
Department of Biology, Galton Laboratory, University College London, London, England
Mol Biol Evol 18:1585-92. 2001..The exact distribution assumed for the omega ratio over sites was found not to affect the effectiveness of the LRT...
- Restrictions on biological adaptation in language evolutionNick Chater
Department of Cognitive, Perceptual and Brain Sciences, University College London, London WC1E 6BT, United Kingdom
Proc Natl Acad Sci U S A 106:1015-20. 2009..As suggested by Darwin, the fit between language and its underlying mechanisms arose because language has evolved to fit the human brain, rather than the reverse...
- Counteracting selective regimes and host preference evolution in ecotypes of two species of walking-sticksC P Sandoval
Marine Science Institute, University of California, Santa Barbara 93106, USA
Evolution 59:2405-13. 2005..Our results shed light onto which traits are involved in the initial stages of ecological specialization and ecologically based reproductive isolation...
- Perspective: models of speciation: what have we learned in 40 years?Sergey Gavrilets
Department of Ecology and Evolutionary Biology, Department of Mathematics, University of Tennessee, Knoxville, Tennessee 37996, USA
Evolution 57:2197-215. 2003..Sympatric speciation is promoted if costs of being choosy are small (or absent) and if linkage between the loci experiencing disruptive selection and those controlling assortative mating is strong...
- Does gene flow constrain adaptive divergence or vice versa? A test using ecomorphology and sexual isolation in Timema cristinae walking-sticksP Nosil
Department of Biosciences, Behavioral Ecology Research Group, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
Evolution 58:102-12. 2004..Our findings illustrate how data on mating preferences can help determine the causal associations between trait divergence and levels of gene flow...
- Reduced adaptation of a non-recombining neo-Y chromosomeDoris Bachtrog
Institute of Cell, Animal and Population Biology, University of Edinburgh, UK
Nature 416:323-6. 2002..Our results provide evidence for the importance of sexual recombination for increasing and maintaining the level of adaptation of a population...
- Cloning of mammalian Ire1 reveals diversity in the ER stress responsesX Z Wang
Skirball Institute of Biomolecular Medicine, the Departments of Medicine, Cell Biology and the Kaplan Cancer Center, NYU Medical Center, New York, NY 10016, USA
EMBO J 17:5708-17. 1998..These results indicate that a single upstream component, Ire1, plays a role in multiple facets of the ER stress-response in mammalian cells...
- Hotter is better and broader: thermal sensitivity of fitness in a population of bacteriophagesJennifer L Knies
Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
Am Nat 173:419-30. 2009..We found that the temperature sensitivity of fitness for phages is similar to that for insects...
- Genetic linkage of ecological specialization and reproductive isolation in pea aphidsD J Hawthorne
Department of Entomology, University of Maryland, College Park 20742, USA
Nature 412:904-7. 2001..This type of genetic architecture may be common in taxa that have speciated under divergent natural selection...
- EvolvabilityPaul D Sniegowski
Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 6018, USA
Curr Biol 16:R831-4. 2006
- How much of the variation in adaptive divergence can be explained by gene flow? An evaluation using lake-stream stickleback pairsAndrew P Hendry
Redpath Museum and Department of Biology, McGill University, Montreal, Quebec H3A 2K6, Canada
Evolution 58:2319-31. 2004..This effect seems relatively unimportant for our system because genetic divergence and gene flow were not correlated with ecologically relevant habitat features of lakes (surface area) or streams (width, depth, flow, canopy openness)...
- Missense meanderings in sequence space: a biophysical view of protein evolutionMark A DePristo
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
Nat Rev Genet 6:678-87. 2005..We then advance a biophysical model of protein evolution that helps us to understand phenomena that range from the dynamics of molecular adaptation to the clock-like rate of protein evolution...
- Quantitative trait locus analyses and the study of evolutionary processDavid L Erickson
Laboratory of Analytical Biology, Smithsonian Institution, Suitland, MD 20746, USA
Mol Ecol 13:2505-22. 2004..Throughout this review we attempt to provide a balanced description of the benefits of QTL methodology to studies in ecology and evolution as well as the inherent assumptions and limitations that may constrain its application...
- The frailty of adaptive hypotheses for the origins of organismal complexityMichael Lynch
Department of Biology, Indiana University, Bloomington, IN 47405, USA
Proc Natl Acad Sci U S A 104:8597-604. 2007....
- Error thresholds and the constraints to RNA virus evolutionEdward C Holmes
Department of Zoology, University of Oxford, South Parks Road, OX1 3PS, Oxford, UK
Trends Microbiol 11:543-6. 2003..Documenting the constraints to RNA virus evolution has important implications for predicting the emergence of new viruses and for improving therapeutic procedures...
- Adaptation and immunityEddie C Holmes
Department of Zoology at the University of Oxford, Oxford, United Kingdom
PLoS Biol 2:E307. 2004
- The evolution of premating isolation: local adaptation and natural and sexual selection against hybridsMaria R Servedio
Department of Biology, CB 3280, Coker Hall, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
Evolution 58:913-24. 2004..I present some situations in which this type of selection is likely to exist. This work also illustrates shortfalls of using a weak selection approach to address questions about reinforcement...
- Adaptive mutation and amplification in Escherichia coli: two pathways of genome adaptation under stressMegan N Hersh
Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Rm S809, Mail Stop 225, Houston, TX 77030 3411, USA
Res Microbiol 155:352-9. 2004..Stress-induced genetic changes may underlie much of microbial evolution, pathogenesis and antibiotic resistance, and also cancer formation, progression and drug resistance...
- Host race formation in the AcariSara Magalhães
Instituto Gulbenkian de Ciencia, Evolutionary Genetics Group, Rua da Quinta Grande, 6, 2780 156 Oeiras, Portugal
Exp Appl Acarol 42:225-38. 2007..We discuss future directions for research on host-associated adaptations in this group of organisms and the potential relevance of host race formation for the biodiversity of mites and ticks...
- Molecular adaptation and the origin of land plantsElizabeth R Waters
Department of Biology, San Diego State University, 5500 Campanile Dr, San Diego, CA 92182 4614, USA
Mol Phylogenet Evol 29:456-63. 2003..In this review I summarize the current knowledge of a variety of physiological and biochemical adaptations to land including plant growth hormones, isoprene, phenolics, and heat shock proteins...
- Synthetic gene recruitment reveals adaptive reprogramming of gene regulation in yeastElad Stolovicki
Department of Physics, Technion Israel Institute of Technology, Haifa 32000, Israel
Genetics 173:75-85. 2006..The results reveal heritable adaptation induced by the exposure to glucose. They demonstrate that genetic regulatory networks have the potential to support highly demanding events of gene recruitment...
- Experimental evidence that predation promotes divergence in adaptive radiationPatrik Nosil
Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada V5A 1S6
Proc Natl Acad Sci U S A 103:9090-5. 2006..Our results indicate that both competition and predation may commonly serve as mechanisms of adaptive radiation...
- Host-range evolution in Aphidius parasitoids: fidelity, virulence and fitness trade-offs on an ancestral hostLee M Henry
Department of Biological Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6 Canada
Evolution 62:689-99. 2008....
- The biological limitations of transcriptomics in elucidating stress and stress responsesM E Feder
Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, IL 60637, USA
J Evol Biol 18:901-10. 2005..In view of this outcome, transcriptomics should undergo careful cost-benefit analysis before investigators deploy it in studies of stress responses and their evolution...
- Adaptation and diversification on islandsJonathan B Losos
Museum of Comparative Zoology, 26 Oxford Street, Harvard University, Cambridge, Massachusetts 02138, USA
Nature 457:830-6. 2009..For these reasons, island research provides valuable insights into speciation and adaptive radiation, and into the relative importance of contingency and determinism in evolutionary diversification...
- Local adaptation and vector-mediated population structure in Plasmodium vivax malariaDeirdre A Joy
Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
Mol Biol Evol 25:1245-52. 2008....
- Adaptive dynamics of dormancy duration variability: evolutionary trade-off and priority effect lead to suboptimal adaptationSébastien Gourbière
Université de Perpignan Via Domitia UMR 5244 CNRS EPHE UPVD, Laboratoire de Biologie et d Ecologie Tropicale et Méditerranéenne, 52 Avenue Paul Alduy, 66860 Perpignan Cedex, France
Evolution 63:1879-92. 2009..Such "evolutionary priority effect" could drive the evolution of maladapted levels of diapause-duration variability...
- The specificity and polymorphism of the MHC class I prevents the global adaptation of HIV-1 to the monomorphic proteasome and TAPBoris V Schmid
Institute of Theoretical Biology, Utrecht University, Utrecht, The Netherlands
PLoS ONE 3:e3525. 2008..We estimate that upon transmission of a virus to a new host 39%-66% of the mutations that caused epitope precursor escapes are released from immune selection pressure...
- Capturing the superorganism: a formal theory of group adaptationA Gardner
Institute of Evolutionary Biology, University of Edinburgh, King s Buildings, Edinburgh, UK
J Evol Biol 22:659-71. 2009....
- Maximum-likelihood analysis of molecular adaptation in abalone sperm lysin reveals variable selective pressures among lineages and sitesZ Yang
Galton Laboratory, Department of Biology, University College London, London, England
Mol Biol Evol 17:1446-55. 2000..Sites under potential diversifying selection were identified. Ancestral lysins were inferred to trace the route of evolution at individual sites and to provide lysin sequences for future laboratory studies...
- Genetic and fitness changes accompanying adaptation of an arbovirus to vertebrate and invertebrate cellsS C Weaver
Center for Tropical Diseases and Department of Pathology, University of Texas Medical Branch, Galveston, Texas 77555, USA
J Virol 73:4316-26. 1999..Our results suggest that alternating host transmission cycles constrain the evolutionary rates of arboviruses but not their fitness for either host alone...
- The evolution of Müllerian mimicryThomas N Sherratt
Department of Biology, Carleton University, Ottawa, Ontario, Canada
Naturwissenschaften 95:681-95. 2008..I highlight areas for future enquiry, including the possibility of Müllerian mimicry systems based on profitability rather than unprofitability and the co-evolution of defence...
- Adaptive mutations in bacteria: high rate and small effectsLilia Perfeito
Instituto Gulbenkian de Ciencia, Rua da Quinta Grande, Number 6, 2780 156 Oeiras, Portugal
Science 317:813-5. 2007..Such a high rate of adaptive evolution has implications for the evolution of antibiotic resistance and pathogenicity...
- The interaction of sexually and naturally selected traits in the adaptive radiations of cichlid fishesWalter Salzburger
Zoological Institute, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
Mol Ecol 18:169-85. 2009....
- Understanding the adaptation of Halobacterium species NRC-1 to its extreme environment through computational analysis of its genome sequenceS P Kennedy
Center of Marine Biotechnology, University of Maryland Biotechnology Institute, Baltimore, Maryland 21202, USA
Genome Res 11:1641-50. 2001..5) GC-skew analysis showed evidence for the existence of two replication origins in the large chromosome. This finding and the occurrence of multiple chromosomes indicate a dynamic genome organization with eukaryotic character...
- Towards a theory of biological robustnessHiroaki Kitano
Mol Syst Biol 3:137. 2007
- The evolution of müllerian mimicry in multispecies communitiesChristopher D Beatty
Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
Nature 431:63-6. 2004..This need to simplify decision making readily facilitates the spread of imperfect mimetic forms from rarity, and suggests that müllerian mimicry is more likely to arise in multispecies communities...
- A scan for signatures of positive selection in candidate loci for skin pigmentation in humansNeskuts Izagirre
Department Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country, Leioa, Bizkaia, Spain
Mol Biol Evol 23:1697-706. 2006....
- Are adaptation costs necessary to build up a local adaptation pattern?Sara Magalhães
Laboratoire de Génétique et Environnement, Institut des Sciences de l Evolution, Universite de Montpellier II, Place Eugène Bataillon Bâtiment 22 cc65, 34095 Montpellier, France
BMC Evol Biol 9:182. 2009..The occurrence of such trade-offs is inferred by a pattern of local adaptation, i.e., a negative correlation between relative performance on different hosts...
- Over the falls? Rapid evolution of ecotypic differentiation in steelhead/rainbow trout (Oncorhynchus mykiss)Devon E Pearse
Fisheries Ecology Division, Southwest Fisheries Science Center, NOAA National Marine Fisheries Service, Santa Cruz, CA 95060, USA
J Hered 100:515-25. 2009..These results support a hypothesis of rapid evolution of a purely resident life history in the above-barrier population in response to strong selection against downstream movement...
- Age of cichlids: new dates for ancient lake fish radiationsMartin J Genner
Department of Biological Sciences, University of Hull, Cottingham Road, Hull HU6 7RX, UK
Mol Biol Evol 24:1269-82. 2007....
- Gene gain and gene loss in streptococcus: is it driven by habitat?Pradeep Reddy Marri
Department of Biology, McMaster University, Hamilton, Ontario, Canada
Mol Biol Evol 23:2379-91. 2006..We have analyzed here some of the experimentally characterized species-specific genes that have been acquired by LGT and conclude that at least a portion of these genes have a role in adaptation...
- How does resource supply affect evolutionary diversification?Alex R Hall
Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Ashworth Laboratories, West Mains Road, Edinburgh EH9 3JT, UK
Proc Biol Sci 274:73-8. 2007..These processes may underlie some general patterns of diversity, including latitudinal gradients in species richness and the effects of anthropogenic enrichment of the environment...
- Adaptive molecular evolution for 13,000 phage generations: a possible arms raceHolly A Wichman
Department of Biological Sciences, University of Idaho, Moscow, 83844 3051, USA
Genetics 170:19-31. 2005..We instead suggest that continuing molecular evolution reflects a potentially indefinite arms race, stemming from high levels of co-infection and the resulting conflict among genomes competing within the same cell...
- Distributions of epistasis in microbes fit predictions from a fitness landscape modelGuillaume Martin
Centre d écologie fonctionnelle et évolutive Centre National de la Recherche Scientifique UMR 5175, 1919 Route de Mende, 34293 Montpellier, France
Nat Genet 39:555-60. 2007..This model may offer a simple and widely applicable alternative to complex metabolic network models, in particular for making evolutionary predictions...
- A single amino acid mutation contributes to adaptive beach mouse color patternHopi E Hoekstra
Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
Science 313:101-4. 2006..Here, we link a single mutation in the coding region of a pigmentation gene to adaptive quantitative variation in the wild...
- Using genome scans of DNA polymorphism to infer adaptive population divergenceJay F Storz
Department of Biology, San Francisco State University, 1600 Holloway Avenue, San Francisco, CA 94132, USA
Mol Ecol 14:671-88. 2005..Finally, I consider the evolutionary and functional insights that might be gained by conducting genome scans for loci involved in adaptive population divergence...
- Biological and biomedical implications of the co-evolution of pathogens and their hostsMark E J Woolhouse
Centre for Infectious Diseases, College of Medicine and Veterinary Medicine, University of Edinburgh, Easter Bush, Roslin, Midlothian EH25 9RG, UK
Nat Genet 32:569-77. 2002....
- The first metazoa living in permanently anoxic conditionsRoberto Danovaro
Department of Marine Science, Faculty of Science, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
BMC Biol 8:30. 2010..Deep seas include some of the most extreme ecosystems on Earth, such as the deep hypersaline anoxic basins of the Mediterranean Sea. These are permanently anoxic systems inhabited by a huge and partly unexplored microbial biodiversity...
- Facilitated variation: how evolution learns from past environments to generalize to new environmentsMerav Parter
Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
PLoS Comput Biol 4:e1000206. 2008..Thus, environments that change in a systematic, modular fashion seem to promote facilitated variation and allow evolution to generalize to novel conditions...
- Bacterial metapopulations in nanofabricated landscapesJuan E Keymer
Department of Physics, Princeton University, Princeton, NJ 08544 1014, USA
Proc Natl Acad Sci U S A 103:17290-5. 2006..Our results illustrate the potential lying at the interface between nanoscale biophysics and landscape evolutionary ecology...
- Positive selection at the protein network periphery: evaluation in terms of structural constraints and cellular contextPhilip M Kim
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
Proc Natl Acad Sci U S A 104:20274-9. 2007..e., extracellular space or cell membrane). This suggests that the observed positive selection at the network periphery may be due to an increase of adaptive events on the cellular periphery responding to changing environments...
- Parallel genotypic adaptation: when evolution repeats itselfTroy E Wood
Indiana University, 1001 E Third St, Jordan Hall 142, Bloomington, IN 47405, USA
Genetica 123:157-70. 2005....
- Adaptive radiation in microbial microcosmsR Craig MacLean
Department of Biology, McGill University, Montreal QC, Canada
J Evol Biol 18:1376-86. 2005..The implications of microbial selection experiments for evolutionary theory are discussed and future directions of research are proposed...
- Ongoing adaptive evolution of ASPM, a brain size determinant in Homo sapiensNitzan Mekel-Bobrov
Howard Hughes Medical Institute, Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
Science 309:1720-2. 2005..These findings, especially the remarkably young age of the positively selected variant, suggest that the human brain is still undergoing rapid adaptive evolution...
- A phylogenetic test for adaptive convergence in rock-dwelling lizardsLiam J Revell
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
Evolution 61:2898-912. 2007....
- Adaptation of Sindbis virus to BHK cells selects for use of heparan sulfate as an attachment receptorW B Klimstra
Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
J Virol 72:7357-66. 1998..Adaptive mutations, selected during cell culture growth of Sindbis virus, enhance binding and infectivity by allowing the virus to attach by an alternative mechanism that is dependent on the presence of cell surface HS...
- Multiple pathways of selected gene amplification during adaptive mutationElisabeth Kugelberg
Section of Microbiology, College of Biological Sciences, University of California, Davis, CA 95616, USA
Proc Natl Acad Sci U S A 103:17319-24. 2006..These findings are relevant to genetic adaptation in any biological systems in which fitness can be increased by adding gene copies (e.g., cancer and bacterial drug resistance)...
- Microbial experiments on adaptive landscapesNick Colegrave
Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK
Bioessays 27:1167-73. 2005..Laboratory populations of microbes allow evolution to be observed in real time and, as such, provide key insights into the topology of adaptive landscapes...
- The rate of compensatory mutation in the DNA bacteriophage phiX174Art Poon
Division of Biological Sciences, Section of Ecology, Behavior and Evolution, University of California, San Diego, California 92093 0116, USA
Genetics 170:989-99. 2005..We estimate that about half of all compensatory mutations are located extragenically in this organism...
- Comparative analysis of morphological diversity: does disparity accumulate at the same rate in two lineages of centrarchid fishes?David C Collar
Section of Evolution and Ecology, University of California, Davis 95616, USA
Evolution 59:1783-94. 2005..4 and 7.7 times greater in Lepomis. Thus, time and phylogeny do not account for the differences in morphological disparity observed in Lepomis and Micropterus, and other diversity-promoting mechanisms should be investigated...
- Properties of adaptive walks on uncorrelated landscapes under strong selection and weak mutationDarin R Rokyta
Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
J Theor Biol 243:114-20. 2006..As in Orr's original model, these results are insensitive to both the distribution of fitness effects and most biological details of the system under consideration...
- Spontaneous emergence of modularity in a model of evolving individualsJun Sun
Department of Physics and Astronomy and Department of Bioengineering, Rice University, Houston, Texas 77005 1892, USA
Phys Rev Lett 99:228107. 2007..We suggest that the hierarchical structure observed in the natural world may be a broken-symmetry state, which generically results from evolution in a changing environment...
- Adaptive value of sex in microbial pathogensRichard E Michod
Department of Ecology and Evolutionary Biology, University of Arizona, Tucson 85721, USA
Infect Genet Evol 8:267-85. 2008..For example, antibiotic resistance may be transferred by bacterial sex, but this transfer is probably not the reason sex evolved in bacteria...
- Extensive genome rearrangements and multiple horizontal gene transfers in a population of pyrococcus isolates from Vulcano Island, ItalyJames R White
University of Maryland, College Park, Maryland, USA
Appl Environ Microbiol 74:6447-51. 2008..The results illustrate the dynamic nature of the genomes of the genus Pyrococcus and raise the possibility of a connection between rapidly changing environmental conditions and adaptive genomic properties...
- Tempo and mode of evolutionary radiation in iguanian lizardsLuke J Harmon
Department of Biology, Campus Box 1137, Washington University, St Louis, MO 63130 4899, USA
Science 301:961-4. 2003..This inverse relationship between timing of diversification and morphological disparity within subclades may be a general feature that transcends the historically contingent properties of different evolutionary radiations...
- Evolutionary genomics of host adaptation in vesicular stomatitis virusSusanna K Remold
Department of Biology, University of Louisville, USA
Mol Biol Evol 25:1138-47. 2008..We discuss the degree to which current genetic architecture is expected to constrain future evolution of complex traits, such as host use by RNA viruses...
- Deterministic and stochastic regimes of asexual evolution on rugged fitness landscapesKavita Jain
Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
Genetics 175:1275-88. 2007..We argue that our findings are relevant to the interpretation of evolution experiments with microbial populations...
- Protein evolution in deep sea bacteria: an analysis of amino acids substitution ratesStefano Campanaro
CRIBI Biotechnology Centre, Department of Biology, University of Padua, Via U Bassi 38 b, 35121, Padua, Italy
BMC Evol Biol 8:313. 2008..To verify this hypothesis we computed the amino acid substitution rates between two deep-sea microorganisms, Photobacterium profundum SS9 and Shewanella benthica KT99, and their respective shallow water relatives...
- Comprehensive mutation identification in an evolved bacterial cooperator and its cheating ancestorGregory J Velicer
Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany
Proc Natl Acad Sci U S A 103:8107-12. 2006..These results provide insight into the genetic basis of two large adaptive transitions in a social bacterium...
- Role of the mutant spectrum in adaptation and replication of West Nile virusAlexander T Ciota
Wadsworth Center, New York State Department of Health, Albany, NY 12201, USA
J Gen Virol 88:865-74. 2007..These data provide evidence of the importance of quasispecies dynamics in the adaptation of a flavivirus to new and changing environments and hosts, with little evidence of significant genetic change...
- Transient and heritable mutators in adaptive evolution in the lab and in natureS M Rosenberg
Department of Biochemistry, University of Alberta, Edmonton, Canada
Genetics 148:1559-66. 1998....
- Viral ecology and the maintenance of novel host useJohn J Dennehy
Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA
Am Nat 167:429-39. 2006..We argue that this effect should facilitate adaptation by the virus to utilize the novel host--often crucial in subsequent phases of emergence...
- Evolution of antioxidant defence mechanismsI F Benzie
Department of Nursing and Health Sciences, Hong Kong Polytechnic University, Kowloon, China
Eur J Nutr 39:53-61. 2000..Finally, suggested benefits underlying our curious inability to manufacture ascorbic acid, and the possible role of uric acid in human antioxidant defence, are briefly discussed with particular reference to nutrition and toxicology...
- Optimization of inclusive fitnessAlan Grafen
St John s College, Oxford OX1 3JP, UK
J Theor Biol 238:541-63. 2006..Important questions remain to be answered in the fundamental theory of inclusive fitness...
- Ecological and evolutionary diversification of the seed beetle genus Stator (Coleoptera: Chrysomelidae: Bruchinae)Geoffrey E Morse
Department of Entomology, One Shields Avenue, University of California, Davis, CA 95616, USA
Evolution 59:1315-33. 2005..The results of this study show that diversification is structured by interactions between different selective pressures and along multiple ecological axes...
- A minimum on the mean number of steps taken in adaptive walksH Allen Orr
Department of Biology, University of Rochester, Rochester, NY 14627, U S A
J Theor Biol 220:241-7. 2003..Put differently, evolution must try out at least e wild-type sequences during an average bout of adaptation...
- Testing hypotheses about ecological specialization using phylogenetic treesP Nosil
Department of Biosciences, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
Evolution 59:2256-63. 2005..Most generally, inferences regarding character evolution can be strengthened by comparing models of character change and examining ancestor states, rather than only comparing parameter values...
- Ecology. Making sense of evolution in an uncertain worldVincent A A Jansen
School of Biological Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
Science 309:2005-7. 2005
- Experimental evolution and genome sequencing reveal variation in levels of clonal interference in large populations of bacteriophage phiX174Kim M Pepin
Department of Biological Sciences, University of Idaho, Moscow, ID, 83844 3051, USA
BMC Evol Biol 8:85. 2008..Genomic sequences of multiple individuals from evolved populations were used to detect competing beneficial mutations...
- The adaptive landscape as a conceptual bridge between micro- and macroevolutionS J Arnold
Department of Zoology, Oregon State University, Corvallis 97331, USA
Genetica 112:9-32. 2001..We also sketch an agenda of empirical issues that is inspired by theoretical developments...
- Compensatory mutations, antibiotic resistance and the population genetics of adaptive evolution in bacteriaB R Levin
Department of Biology, Emory University, Atlanta, Georgia 30322, USA
Genetics 154:985-97. 2000....
- The evolution of bet-hedging adaptations to rare scenariosOliver D King
Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA
Theor Popul Biol 72:560-75. 2007..In this case, the approximate requirements for bet-hedging to be favored by a ratio of at least R are that sN>log(R) and thetaN>square root R ...
- Maladaptation and the paradox of robustness in evolutionSteven A Frank
Department of Ecology and Evolutionary Biology, University of California at Irvine, Irvine, California, United States of America
PLoS ONE 2:e1021. 2007..Such buffering mechanisms are often discussed in terms of robustness, which may be measured by reduced sensitivity of performance to perturbations...
- Spatial mosaic formation through frequency-dependent selection in Müllerian mimicry complexesThomas N Sherratt
Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON, Canada K1S 5B6
J Theor Biol 240:165-74. 2006..Overall, this model highlights how a stable mosaic of different mimetic forms can evolve from a range of starting conditions through a combination of chance effects and localized frequency-dependent selection...
- Adaptive evolution of fertilization proteins within a genus: variation in ZP2 and ZP3 in deer mice (Peromyscus)Leslie M Turner
Division of Biological Sciences, University of California, San Diego, USA
Mol Biol Evol 23:1656-69. 2006..These findings demonstrate that the pattern of adaptive reproductive protein evolution found at higher taxonomic levels can be documented between closely related mammalian species, where reproductive isolation has evolved recently...
- Widespread adaptive evolution of Drosophila genes with sex-biased expressionMatthias Pröschel
Section of Evolutionary Biology, Department of Biology II, University of Munich LMU, 82152 Munich, Germany
Genetics 174:893-900. 2006..melanogaster and D. simulans. This suggests that sexual selection and intersexual coevolution are the major forces driving genetic differentiation between species...
- The genetics of adaptation in Drosophila sechelliaCorbin D Jones
Department of Biology, Carolina Center for Genome Science, University of North Carolina, Chapel Hill, NC 27599, USA
Genetica 123:137-45. 2005..The data from D. sechellia suggest that adaptations are not as genetically complex as historically thought, although almost all of the adaptations of D. sechellia involve several genes...
- Mechanisms of checkpoint kinase Rad53 inactivation after a double-strand break in Saccharomyces cerevisiaeGhislaine Guillemain
CEA, Direction des Sciences du Vivant, Institut de Biologie et de la Technologies de Saclay, 91191 Gif sur Yvette Cedex, France
Mol Cell Biol 27:3378-89. 2007..Our data thus strongly suggest that CK2 is the kinase responsible for the in vivo phosphorylation of Ptc2 T376...
- Fitness effects of beneficial mutations: the mutational landscape model in experimental evolutionAndrea J Betancourt
Institute for Evolutionary Biology, King s Buildings, University of Edinburgh, Edinburgh, EH9 3JT, UK
Curr Opin Genet Dev 16:618-23. 2006....
- Evidence of viral adaptation to HLA class I-restricted immune pressure in chronic hepatitis C virus infectionSilvana Gaudieri
Centre for Clinical Immunology and Biomedical Statistics, Level 2, North Block, Royal Perth Hospital, Wellington St, Perth, Western Australia 6000, Australia
J Virol 80:11094-104. 2006..This analysis of host-virus interaction reveals evidence of HCV adaptation to HLA class I-restricted immune pressure and identifies in vivo targets of cellular immune responses at the population level...
- History and the global ecology of squamate reptilesLaurie J Vitt
Sam Noble Oklahoma Museum of Natural History and Zoology Department, University of Oklahoma, Norman, Oklahoma 73072, USA
Am Nat 162:44-60. 2003..These historically derived niche differences are apparent in extant lizard assemblages and account for some observed structure. These patterns occur in a variety of habitats at both regional and local levels throughout the world...
- Staining Techniques for Micro-CT Imaging of MicrodamageRYAN ROEDER; Fiscal Year: 2004..From a biological adaptation standpoint, damage with the bone tissue is believed to stimulate remodeling...
- Statistical Studies of Genomic EvolutionMasatoshi Nei; Fiscal Year: 2009..of multigene families arid the origins of new genes and new genetic systems that are important for biological adaptation. In the next grant period we will focus on the evolution of the primate KIR and the rodent Ly49 gene ..
- Towards a general theory of evolutionary capacitanceJoanna Masel; Fiscal Year: 2009..Since direct experiments on capacitance cannot be performed in humans, the theoretical and predictive approach described here is particularly important for understanding the scope of capacitance in explaining human variation. ..
- BIOSYNTHESIS OF VITAMIN B12 AND ANAEROBIC METABOLISMJohn Roth; Fiscal Year: 2004..coli. Understanding this metabolism may contribute to understanding the natural lifestyle of Salmonellae. ..
- Gene Duplication and Genome EvolutionAustin Hughes; Fiscal Year: 2004..5) Examining the role of transposable elements in duplication of genomic segments by testing for nonrandom association between these elements and putatively duplicated blocks in the yeast genome. ..
- JWatcher-event recorder and behavioral analysis programDANIEL BLUMSTEIN; Fiscal Year: 2004..While we will continue to freely-distribute the software, on-going support and routine updates will be supported by the sales of a detailed users manual, which will include laboratory exercises suitable for teaching. ..
- Molecular mechanism of DNA-polymerase choice in vivoSusan Rosenberg; Fiscal Year: 2007..coli DNA polymerases, and functions in DNA polymerase choice in vivo: a critical regulatory decision for cell survival of environmental damage, and genomic health. [unreadable] [unreadable] [unreadable]..
- ECOLOGY AND GENETICS OF VENEZUELAN EQUINE ENCEPHALITISScott Weaver; Fiscal Year: 2005..This information will be invaluable in targeting prevention and control resources, especially for obtaining maximum benefit in developing countries with limited resources. ..
- DNA REPAIR IN DRUG RESISTANCE MUTATIONSusan Rosenberg; Fiscal Year: 2003....
- WORKSHOPS IN FORMAL DEMOGRAPHY AND BIODEMOGRAPHYShripad Tuljapurkar; Fiscal Year: 2008..unreadable] DESCRIPTION (provided by applicant): Applicant did not provide description. [unreadable] [unreadable] [unreadable]..
- SECRETIONS OF ARTHROPODSThomas Eisner; Fiscal Year: 2008..Insects are major vectors of disease. An understanding of how insects depend on natural products for regulation of their biotic interactions is of broad applied significance to both medicine and agriculture. [unreadable] [unreadable]..
- PATHOGENIC ADAPTATION OF MICROBIAL ADHESINSEVGENI VENIAMINOVIC SOKURENKO; Fiscal Year: 2010..Studies proposed here will serve as model ones to provide a spectrum of novel information regarding shear effects on bacterial adhesion, particularlyin connection to the bacterial pathogenesis. ..
- Evolutionary genomics of new Drosophila genesDAVEN PRESGRAVES; Fiscal Year: 2004..The methods developed will be applicable in comparative analysis of other genomes, including those of humans and their primate relatives. ..
- Evolution of vertebrate sensory genesJianzhi Zhang; Fiscal Year: 2010..These studies will also help understand human smell and taste variations and disorders. ..
- Mechanisms of Adaptive AmplificationPhilip J Hastings; Fiscal Year: 2010....
- Mammalian Genomes - Stasis and ChangeHOLLY WICHMAN; Fiscal Year: 2009..This proposal will also ask whether changes in patterns of methylation by endocrine disruptors is linked to increased rates of retrotransposition. ..
- EVOLUTION OF IMMUNE RECOGNITION AND EVASIONAustin L Hughes; Fiscal Year: 2010..In addition, by increasing our understanding of the population diversity and evolutionary history of human immune system genes, this research will enhance our knowledge of human immune function in health and disease. ..
- "WORKSHOPS IN FORMAL AND QUANTITATIVE DEMOGRAPHY"Shripad Tuljapurkar; Fiscal Year: 2005..Second, a three-day Mini-workshop in advanced modeling and analysis organized around specialized topics (forecasting in year 1, biodemographic models in year 2). ..
- EID - Effects of avian migration & anthropogenic change on the distribution & traThomas Smith; Fiscal Year: 2009..Finally, we will share our results with public health organizations and the scientific community in a timely fashion in order to maximize the public good. ..
- Pathways of T cell SenescenceABBE DE VALLEJO; Fiscal Year: 2009....
- Agilent 6890 GC/5973 mass detector for ProfilingRoger Davis; Fiscal Year: 2005..The projected use of each investigator is shown in table 1 and will account for 100% time use. Therefore, we have no alternative equipment for this essential technique. ..
- Interdisciplinary Study of Acid-Meditated Tumor InvasionRobert Gatenby; Fiscal Year: 2005..Perturbations that produce slowing or reversal of the traveling wave solution to the state equations (ie tumor growth) will be explored to predict possible new treatment strategies. ..
- SLEEP ACADEMIC AWARD--RECOGNITION OF SLEEP DISORDERSKingman Strohl; Fiscal Year: 2002..We will disseminate of educational assessments, patient-oriented material, and clinical pathways through local and national consultants in both the public and private sector, as well as through interaction with other awardees. ..
- Transcriptional Coactivators in Liver FunctionJanardan Reddy; Fiscal Year: 2008..These studies are expected to generate new information, with implications for human impact, which could provide novel avenues for developing strategies to regulate gene function by altering coactivator activity. ..
- Regulation of Pregnancy-Dependent AdaptationsMichael Soares; Fiscal Year: 2009..Novel ideas and a novel research approach have been presented to elucidate regulatory mechanisms controlling fundamental processes essential for the establishment and maintenance of pregnancy. ..
- NEUROENDOCRINE/IMMUNE INTERACTIONS: ROLE OF MELATONINSTEVEN YELLON; Fiscal Year: 2002....
- P.Gingivalis and Oral Keratinocyte-ECM InteractionsVito Quaranta; Fiscal Year: 2004..g. may initiate and sustain periodontal disease. Such clues may be useful for devising new modalities of treatment and prevention. ..
- Interdisciplinary Training in Genetics and Complex Disease(RMI)Marianne Wessling Resnick; Fiscal Year: 2008..abstract_text> ..
- Models of Sensory CodingMichael Leon; Fiscal Year: 2008..These experiments should help us understand the mechanism by which the olfactory nervous system codes complex stimuli. ..
- INTRAUTERINE ASPHYXIAL ENCEPHALOPATHYPeter Gluckman; Fiscal Year: 2001..By further elucidating the pathogenesis of prenatal and perinatal asphyxial encephalopathy these studies will provide important information towards improving perinatal diagnosis, monitoring and intervention. ..
- FUNCTIONS AND INTERACTIONS OF PRESENILINSKENNETH KOSIK; Fiscal Year: 2003....
- MOLECULAR CHAPERONES OF CLASS I MHCTed Hansen; Fiscal Year: 2003..Our knowledge of the precise mechanism of peptide loading in the ER is key to understanding how viral pathogens abrogate immune recognition and how we might design future protocols for constructive intervention. ..
- Modeling the Spatial Dynamics of Plasmid TransferSTEPHEN KRONE; Fiscal Year: 2009....
- A MODEL SYSTEM FOR PREDICTING EVOLUTIONARY POTENTIALBarry Hall; Fiscal Year: 2003..The resulting mutants will then be characterized to determine which kind of data most accurately predicted the eventual evolutionary outcome. ..
- SLEEP AND ENTERTAIMENT OF SCN FUNCTIONKingman Strohl; Fiscal Year: 2002..abstract_text> ..
- Molecular Regulation of Intergrin FunctionVito Quaranta; Fiscal Year: 2002..Hopefully, with these Aims we will be able to outline a coherent picture as to how Ln-5, integrins and MMP interact to regulate cell adhesion and migration in the context of tissue organization and remodeling. ..
- FASEB Conference: Mechanisms of Liver Growth and DiseaseJanardan Reddy; Fiscal Year: 2002..abstract_text> ..
- ROLE OF NITRIC OXIDE IN FERTILIZATIONDavid Epel; Fiscal Year: 2002..The possible role of NO in regulating the egg's ion channels (as part of polyspermy block) and sperm physiology (such as motility and the acrosome reaction) will also be investigated. ..
- Functional Genomics of Cryptosporidium parvumGiovanni Widmer; Fiscal Year: 2007..parvum. A comparison of the host cell response to C. parvum type 1 and type 2 will be performed to probe the molecular basis of the observed difference in virulence between types. ..
- APO B TRANSLOCATION AND DEGRADATIONRoger Davis; Fiscal Year: 2007..We are confident that our proposed studies will provide new insights that will add further proof to the feasibility and advance the therapeutic potential of controlling the apo B processing pathway. ..
- Development of Cdk5 InhibitorsKENNETH KOSIK; Fiscal Year: 2007..Because compound validation requires a broad expertise that is unlikely to be present in a single lab we have assembled individuals who collectively have the expertise to complete the aims. ..
- The Rate and Molecular Spectrum of Spontaneous MutationsMichael Lynch; Fiscal Year: 2009....
- MATERNAL ADAPTATIONS TO PREGNANCYMichael Soares; Fiscal Year: 2001..abstract_text> ..
- EVOLUTIONARY GENETICS OF VERTEBRATE VISIONShozo Yokoyama; Fiscal Year: 2002..abstract_text> ..
- Role of Leptin in Systemic Lupus ErythematosusAntonio La Cava; Fiscal Year: 2010..This study will detail the effects of leptin on human lupus and compare the potential of different leptin-based approaches with the goal to improve the current therapeutic management of human lupus. ..
- Role of Microstructure in Nanomechanical Behavior of Bone TissueMarjolein C van der Meulen; Fiscal Year: 2010..Our approach will cross-correlate several microlevel techniques that have not been previously used to characterize bone tissue mechanics. ..
- Genes controlling heart function in a hibernating mammalMatthew Andrews; Fiscal Year: 2005..abstract_text> ..
- A Genomic Study of Sex-Role and Social DominanceSUSAN RENN; Fiscal Year: 2006..In addition to evolutionary implications, these studies will inform further hypotheses to be tested through functional analysis. ..
- A Wireless, Multi-Channel Telemetric Biosensor for Research in Animal ModelsKingman Strohl; Fiscal Year: 2006..The proposed research will facilitate animal studies that may lead to a better understanding of sleep disorders and potentially new interventions. [unreadable] [unreadable] [unreadable]..
- Fluorescence-based screen to probe hepcidin-ferroportin interactionsMarianne Wessling Resnick; Fiscal Year: 2006..The project has broader applicability in the development of HTS to assay ligand-receptor interactions as well as representing a major advance towards the discovery of small molecule probes of iron transport. ..
- LYMPHOCYTE RECEPTORS FOR VASOACTIVE INTESTINAL PEPTIDEEDWARD GOETZL; Fiscal Year: 2007..abstract_text> ..
- MOLECULAR GENETICS OF THERMOGENESISLESLIE KOZAK; Fiscal Year: 2007..Concurrent with gene identification, the experiments will provide phenotypic information on how these genes affect the development of excessive adiposity. ..
- Aquaporin 5 (AQP5) in Lung Fluid HomeostasisCARISSA KRANE; Fiscal Year: 2004..This combinatorial approach will provide valuable information for the identification of new mechanistic pathways critical for the development of novel drug targets for the treatment of asthma. ..
- GENETICS OF DEVELOPMENTAL PLASTICITY IN THE ADIPOCYTELESLIE KOZAK; Fiscal Year: 2004..Finally (Aim 5), candidate cDNAs or genes will be tested by complementation in a cell culture system based on preadipocytes or BAC transgenesis using B6.A congenics. ..
- Experimental tests of vocal learning in songbirdsDavid Lahti; Fiscal Year: 2007..abstract_text> ..
- Ex Vivo Delineation of Mechanisms of Cerebral VasospasmJAY HUMPHREY; Fiscal Year: 2008..In summary, we submit that this project will reveal new insight into mechanisms. ..
- Development of RNAi as Treatment for NeurodegenerationKENNETH KOSIK; Fiscal Year: 2005..These experiments open the way for the Colombian scientists to participate directly in the next phase of the research beyond descriptive genetics in which the Colombian group has made such a strong contribution. ..
- Novel Organ Culture & Theory for Arteriolar RemodelingJAY HUMPHREY; Fiscal Year: 2005..We will collect simultaneous pressure-diameter, cell morphological, and actin cytoskeletal data at multiple times during the remodeling, which in turn will allow us to develop a novel, single theoretical framework. ..
- Compound Identification in Assays for Tau PathologyKENNETH KOSIK; Fiscal Year: 2004..This proposal principally involves work at two sites. They are the Kosik laboratory in the Center for Neurologic Diseases and the Laboratory for Drug Discovery for Neurodegeneration (LDDN) under the direction of Ross Stein. ..
- The Regulation of Neuronal miRNA ExpressionKENNETH KOSIK; Fiscal Year: 2004..In particular, impaired neuronal polarity acquisition, synaptogenesis, and translation of specific mRNAs are possible phenotypic outcomes of Dicer suppression. ..
- International Conference on Molecular Systems BiologyMichael Savageau; Fiscal Year: 2004..Contributions are accepted based on peer review by a 14-member Scientific Committee. Selected papers will be proposed for further review and, if accepted, subsequent publication in a special issue of Mathematical Biosciences. ..